Friday, December 18, 2015

Now HIRING! Looking for passionate graduate students and post doctoral fellows

My group is currently recruiting people to fill two graduate student positions. We will also be recruiting a researcher to fill a postdoctoral position in the coming year.

We are looking for candidates who are passionate about genetics, genomics, and research. Ideal candidates are creative, hard working (while maintaining a work/life balance), and self starters. Our group is strictly computational, so candidates should enjoy working on computers and analyzing data. Candidates should be willing to learn programming (typically in R or Python), or already have some programming experience.

We will soon have access to over 200,000 genotyped beef cattle with phenotypes and breeding values. We also have access to whole genome sequencing data from over 2,000 cattle. So, if you like working with lots of data, come join us! Our group uses population genomics to better understand the  history of cattle breeds and to inform future selection decisions. We are interested in local genetic adaption, fertility, inbreeding, and, of course, genomic prediction. With our collaborators, we also enjoy projects looking at the evolution of quail, dogs, and catfish.

Interested candidates are encouraged to apply to the Division of Animal Sciences, the Genetics Area Program, or the Informatics Institute. The deadline to apply to the Division of Animal Sciences and be considered for all fellowships if February 1st. The deadline to apply to the Genetics Area Program is January 15th. Deadline for the Informatics Institute is March 1st.

As a graduate mentor, my focus is helping you achieve your career goals. I have an open door policy and routinely touch base with my students. We have weekly joint lab meetings with Jerry Taylor's group. I have an annual meeting with each student to discuss career plans, 5 and 10 year plans, degree progress, professional development goals, etc. I would be happy to put you in touch with my current graduate students so they can tell you more about my mentorship style and what working in my group is like.

Please contact me if you would like more information about these positions.




The University of Missouri is an Equal Opportunity/Affirmative Action employer. To request ADA accommodations, please contact Amber Cheek, JD our Director of ADA Education and Accessibility at 573-884-7278 (V/TTY).


Wednesday, December 9, 2015

GENOMICS: Where are we going?

Photo by Lana Eaton, Eaton Charolais, Lindsay, Mont.
Cover by Molly Schoen
The June/July issue of the Charolais Journal contained an article I wrote.

Click this link to download a copy of the article.

In the article I discuss trends I see coming in the development of genomic prediction. Please provide feedback in the anonymous survey below.


Tuesday, December 8, 2015

Pigs that are Resistant to Incurable Disease Developed at University of Missouri

Discovery about PRRS virus could save swine industry hundreds of millions of dollars; Exclusive deal signed with global leader in animal genetics

COLUMBIA, Mo. ­— Porcine Reproductive and Respiratory Syndrome (PRRS) virus was first detected in the U.S. in 1987. Pigs that contract the disease have extreme difficulty reproducing, don’t gain weight and have a high mortality rate. To date, no vaccine has been effective, and the disease costs North American farmers more than $660 million annually. Now, a team of researchers from the University of Missouri, Kansas State University, and Genus plc have bred pigs that are not harmed by the disease.


Prather PRRS from MU News Bureau on Vimeo.


“Once inside the pigs, PRRS needs some help to spread; it gets that help from a protein called CD163,” said Randall Prather, distinguished professor of animal sciences in the College of Agriculture, Food and Natural Resources. “We were able to breed a litter of pigs that do not produce this protein, and as a result, the virus doesn’t spread. When we exposed the pigs to PRRS, they did not get sick and continued to gain weight normally.”

For years, scientists have been trying to determine how the virus infected pigs and how to stop it. Previously, researchers believed that the virus entered pigs by being inhaled into the lungs, where it attached to a protein known as sialoadhesin on the surface of white blood cells in the lungs. However, two years ago Prather’s group showed that elimination of sialoadhesin had no effect on susceptibility to PRRS. A second protein, called CD163, was thought to “uncoat” the virus and allow it to infect the pigs. In their current study, Prather’s team worked to stop the pigs from producing CD163.

“We edited the gene that makes the CD163 protein so the pigs could no longer produce it,” said Kristin Whitworth, co-author on the study and a research scientist in MU’s Division of Animal Sciences. “We then infected these pigs and control pigs; the pigs without CD163 never got sick. This discovery could have enormous implications for pig producers and the food industry throughout the world.”

While the pigs that didn’t produce CD163 didn’t get sick, scientists also observed no other changes in their development compared to pigs that produce the protein.

The early-stage results of this research are promising. The University of Missouri has signed an exclusive global licensing deal for potential future commercialization of virus resistant pigs with the Genus, plc. If the development stage is successful, the commercial partner will seek any necessary approvals and registration from governments before a wider market release.

“The demonstration of genetic resistance to the PRRS virus by gene editing is a potential game changer for the pork industry,” said Jonathan Lightner, Chief Scientific Officer and Head of R&D of Genus plc. “There are several critical challenges ahead as we develop and commercialize this technology; however, the promise is clear, and Genus is committed to developing its potential. Genus is dedicated to the responsible exploration of new innovations that benefit the well-being of animals, farmers, and ultimately consumers.”

“At the end of our study, we had been able to make pigs that are resistant to an incurable, untreatable disease,” said Kevin Wells, co-author of the study and assistant professor of animal sciences at MU. “This discovery could save the swine industry hundreds of millions of dollars every year. It also could have an impact on how we address other substantial diseases in other species.”

In addition to Whitworth and Wells, Prather’s research team included collaborators at Genus plc, and Kansas State University. The study, “Gene-edited pigs are protected from porcine reproductive and respiratory syndrome virus,” is being published in Nature Biotechnology this month.

Genus plc, the U.S. Department of Agriculture (USDA) and University of Missouri’s Food for the 21stCentury Program provided funds for the research.

Friday, December 4, 2015

North American Limousin Foundation Releases Recalibrated GE-EPDs

By Joe Epperly, NALF assistant executive director

Limousin breeders and their commercial customers benefit greatly from new breeding and selection tools. The North American Limousin Foundation (NALF) has launched genomic-enhanced EPDs (GE-EPDs) with the fall 2015 international cattle evaluation. This provides GE-EPDs for all Limousin and Lim-Flex® animals that have completed DNA testing for genomic profiles.

A recalibration in cooperation with GeneSeek® and the Canadian Limousin Association has supplied genomic profiles on more than 4,500 Limousin and Lim-Flex animals. Molecular breeding values from either a high- or low-density genomic profile test are then blended into EPD calculations to produce GE-EPDs. This recalibration has led to the doubling of the number of animals included, the number of traits enhanced, and the genetic correlations.

The advantage to animals with GE-EPDs is increasing EPD accuracy values on many traits equivalent to having 8-20 progeny. This adds greatly to the predictability in selection for genetic merit of young, unproven seedstock. Animals that are genomic-enhanced will have the NALF GE-EPDs displayed on their animal detail screen and performance reports in the NALF-DigitalBeef platform. Traits that are genomic-enhanced are highlighted in yellow on these reports.

"We are excited to offer cutting edge tools for the selection of superior genetics to members and commercial producers purchasing Limousin and Lim-Flex animals. NALF has options for DNA testing that fit both your budget and needs for various traits," says Brittany Barrick, NALF director of registry and performance.

For questions regarding DNA testing options and procedures, contact Brittany Barrack, NALF director of registry and performance at 303-220-1693, ext. 57 or Brittany@NALF.org.

Wednesday, November 25, 2015

Heifer Sale Exceeds Expectations

by Eldon Cole, Livestock Specialist
Headquartered in Lawrence County, MO

The skidding cattle market the past few months resulted in considerable pessimism prior to the 33rd Show-Me-Select (SMS) Bred Heifer Sale at Joplin Regional Stockyards on November 20.  However, when the last of 293 heifers left the ring, the average price of $2477 brought smiles to most of the sellers.

The previous 32 sales results predicted an average heifer price just under $2000 per head.  That forecast is based on the week’s average price per head for a 550 pound, Medium and Large Frame, Number 1 Muscle steer at the Joplin and Springfield markets.  That average amounted to $1011 per head according to the Missouri Market Summary.

The SMS heifer average of $2477 divided by the steer average resulted in a 2.45:1 figure.  In the previous sales the highest ratio was 2.4:1.  Since the SMS sales began in 1997 at Joplin the smallest ratio was 1.65:1 in 1999.

There was a standing room only crowd at the sale along with 254 viewers on DV Auction.  Buyers came from Arkansas, Oklahoma, Kansas and Texas and they took 110 (38%) heifers out of the Show-Me state.

The high-selling heifers for the evening was 5 head from Gilmore Farms, Aurora.  They were F1 Angus-Hereford heifers bred AI to TH 122 711 Victor 719T, a Polled Hereford.  The buyer was David Diggins, Moundville for $3200.  Gilmore topped the overall consignment average with a $2975 price on 8 heifers.

Circle S Chicks, Dusty and Valene Sturgeon, Starks City had the second high consignor average at $2838 for their 40 head of Red Angus heifers bred AI to Bieber Makin’ Hay 9913.  Two buyers each took 20 head, Harold Haskins, Diamond and John G. Harris, Russellville, AR.

John and Janet Massey, Aurora consigned 10, Angus-Simmental heifers that claimed the third high consignor average at $2684.  Following close behind was 38, Angus-Hereford cross heifers from John Wheeler, Marionville that averaged $2651.

The volume buyers of heifers were Harris who took 27 head to Arkansas.  Following him, Haskins ended up with 22 head.

As usual, repeat buyers were abundant with 21 of the 39 buyers being repeat customers. The repeat buyers bought 162 (55%) of the heifers. The 160 head of AI bred heifers sold for $2604 per head. Those bull bred averaged $2325, $279 behind. Only 10 head were tagged Tier Twos and they averaged $2800. Tier Two indicates the heifers were sired by AI bulls who had attained specified EPD accuracy ratings for calving ease direct, calving ease maternal, weaning weight, carcass weight and marbling.

Show-Me-Select cooperators are presently breeding or soon will breed heifers for the May 20 sale in southwest Missouri. For details on how to participate in the value added program contact your University of Missouri extension livestock specialist. Rules and regulations may be found at: http://agebb.missouri.edu/select/prgmreq.htm

Friday, November 13, 2015

Hereford Education Forum: AHA Developments in National Cattle Evaluation

Dorian Garrick
Iowa State University

The Pre-Genomic Era

In the Pan-American Evaluation there are four countries, US, Canada, Uruguay and Argentina. Agricultural Business Research Institute (ABRI) collects the pedigree and trait data. Then the Animal Genetics & Breeding Unit uses BREEDPLAN to estimate EPDs.

To put the number of records turned in to the AHA data in context, we can compare them to other breeds. The 11 breed associations in International Genetic Solutions add 340,000 new animals in each of 2012 and 2013. AGI adds about 300,000 per year. Herefords add a little less than 100,000 animals per year.

The Early-Genomic Era

Cattle have 30 pairs of chromosomes. There are about 100 million base pairs per chromosome and about 2.6 billion base pairs in the entire DNA (genome).

Most errors in chromosome replication are fixed. But, some slip through and are passed down through generations.

The EPD of a bull is a sum of the average gene effects he carries. Until the genomic era, we progeny tested a bull to see how his progeny performed, and thus the gene effects he carries. In genomic prediction we try to use DNA information to estimate the gene effects the bull carries. A good bull has more of the favorable gene effects, and fewer unfavorable gene effects. A bad bull has fewer favorable gene effects and more unfavorable gene effects. But the good bull still carries unfavorable gene effects and can produce bad progeny, based on the chromosomes and genes that progeny inherits.

We tend to think of EPDs associated with an animal. But in genomics we associate an EPD (breeding value) with a segment of DNA to predict the genetic merit of the bull.

In current genomic prediction, we don't test the actual DNA variants causal or responsible for the variation in the trait. We use DNA variants spread throughout the genome. There are relationships between DNA variants on SNP chips and the actual causal variants. We call this relationship linkage disequilibrium. So, even though we are not testing the causal variant, we can use the linkage disequilibrium to predict the causal variant inherited based on the DNA variants in the same chromosome neighborhood.

Using the DNA variants on the SNP chip, Garrick's group came up with a prediction equation. Each SNP gets an effect in this model. The animal's DNA is then tested at GeneSeek, the prediction equation is applied, and a molecular breeding value is calculated. This molecular breeding value is then combined with pedigree and trait data to produce a genomic-enhanced EPD. The American Hereford Association now has over 20,000 animals genotyped. In the last month, 2,000 Hereford animals were genotyped.

Usually a very small portion of a contemporary group was genotyped (usually one or no animals are genotyped per contemporary group). When a larger portion of the contemporary group is genotyped many of the issues (statistical difficulties) with genomic prediction go away.

Make sure an animal has a registration number before doing DNA testing. Make sure the registration number is correct when submitting samples.

If the genotyped sex does not match the recorded sex, Garrick's group doesn't use these genotypes.

Also, we can't use duplicate genotypes. If an animal has multiple DNA tests run, either the failed test is removed, matching genotypes are merged, or if the genotypes don't match, both sets of genotypes are thrown out.

Garrick's group can also do breed verification.

We can also do parentage verification. If the Dam has an AA genotype at a DNA variant, then the calf cannot have a BB genotype at that DNA variant (calf can be AB or AA). Breeds should begin considering testing all animals in the herd. This would allow us to identify unknown parentage, not just verify the reported parentage.

The first SNP test widely used in cattle was the Illumina 50K SNP chip (the earlier Affymetrix chip was not widely adopted). In a hope to use genomic predictions across breeds, a 700K SNP chip was created.

GeneSeek then created a 25K and a 30K chips (GGP LD chips).

GeneSeek also created a 70K chip and later a 150K GGP uHD chip.

Initally, when implementing genomic selection reduced marker panels were created. Pfizer (now Zoetis) recognized they could get a bulk discount on 50K and never released a low density product.

Next step forward

Garrick gave a list of developments he is working on, namely:

  • Single step analyses (no blending or interms).
  • Actual rather than Approximated Accuracies.
  • More regular runs.
  • Readily incorporate new traits.


Bruce Golden and Garrick are creating a new evaluation system called BOLT CUDA evaluation system. At this point in the presentation, Garrick took off his ISU hat and put on his Theta Solutions hat (private company). The difference in this evaluation is the use of graphics cards (GPUs) instead of CPUs. Water cooling systems are also used in GPU systems.
Theta Solutions is currently using computers with 4 graphics cards.

Using a traditional computing, it would take an hour and a half to run an analysis. Using parallel computing, can get this down to 25 minutes. But, with graphic cards, can do this in 1 to 2 minutes.
Using 4.5 million animals can solve genetic predictions for Herefords in less than 12 minutes. It takes another hour to calculate the real accuracies.

Conclusions

Garrick gave five take home points for producers:

  • Genomic analyses are developing rapidly
  • New statistical models
  • New marker panels
  • More animals genotyped
  • New computing resources


Wednesday, November 11, 2015

Hereford Educational Forum: New Traits

Bill Bowman and Sally Northcutt
Method Genetics LLC

Bowman and Northcutt discussed several new EPDs either in development or released by AHA, including:

  • Dry Matter Intake
  • Sustained Cow Fertility
  • Heifer Calving Rate
  • Udder Quality (Teat Size and Udder Suspension)

Heifer Calving Rate, Sustained Cow Fertility, and Dry Matter Intake are currently released as prototype evaluations and can be accessed as a downloadable Excel file.

"One of the things you all have going for you is the foresight to begin a TPR program," said Bowman.

Heifer Calving Rate

Heifer Calving Rate (HCR) is a categorical trait, they either calved or they didn't. Method Genetics reports a heritability of 15% for Heifer Calving Rate. They analyzed 98,000 records, of which 73% had calved by 800 days of age, 27% had not calved. Contemporary grouping for heifers is based upon their herd, yearling weigh date, calf birth year and season.

"This EPD goes beyond a traditional heifer pregnancy EPD." said Northcutt.
Bowman added, "This follows through to calving, which is really what we want."

The higher value is more favorable for the Heifer Calving Rate EPD. If Sire A has a HCR EPD of 8% and Sire B has a HCR EPD of 2%, we would expect 6% more of Sire A's heifers to calve.
The benefits of this EPD include improvement for a lowly heritable trait, provides an opportunity for selection pressure to improve calving, and can now directly include fertility (Heifer Calving Rate) into AHA indexes in the future.

Sustained Cow Fertility

Whole Herd TPR allows a spring board for Heifer Calving Rate, which acts as a first step in looking at Sustained Cow Fertility. Sustained Cow Fertility is a survival analysis that is different from a typical longevity EPD. It uses the Heifer Calving Rate evaluation as the starting point. After this point contemporary groups become dynamic; after calving as a heifer females exposed together make up a contemporary group. Calving intervals and age at calving are calculated. The model accounts for milk and total maternal calving ease EPDs.

A cow is "Successful" until she fails to have a calf. But, some records are "Censored", i.e. the data is handled carefully for exceptions like a cow being sold as a breeding female (registration transferred) or becoming a donor dam. Sustained Cow Fertility has a heritability of 20%.

A higher value is more desirable for sustained cow fertility.

Dry Matter Intake (DMI)

This EPD starts with a multi-trait animal model including:

  • Individual feed intake (standardized)
  • National Cattle Evaluation weaning and yearling weights
  • Four-generation pedigree


Feed intake has a heritability of 40%.
Weaning records are included for contemporaries of calves with an individual intake record to account for selection bias (sending the best calves to feeding test to measure feed intake).

In Dry Matter Intake (DMI) lower values are predictive of less intake. When you begin looking at feed intake, cattle that gain well tend to be more efficient, but they tend to eat more. We want to find outliers who eat less feed but gain more weight. Downloadable Excel spreadsheets contain both DMI EPDs and Yearling Weight EPDs to allow breeders to look at this. Single trait selection should be avoided. Incorporation of Dry Matter Intake genetic values into the AHA indexes will be the greatest benefit.

As we have discussed in the past, depending on how you slice it, feed efficiency rankings can be different and the most effective strategy is an economic index.

Think about the entire system, not a single trait!

Challenging traits are now more accessible from a genetic standpoint. Reproductive traits with lower heritability are addressed. A foundation is established for genomic-enhanced EPDs in these traits.

Udder Quality

In the current udder quality evaluation, it is a standalone evaluation, meaning no other traits are fit in the model, only Udder and Teat scores. Currently there is no genomic component. Since 2008 the genetic trend for udder and teat scores have increased dramatically.

Genetic Trends for breed averages in udder suspension and  teat size EPDs. Data from Fall 2015 AHA Sire Summary.

The genetic correlation between Udder and Teat EPDs is about 0.8. But, this does not mean the udder score should always equal the teat score; in fact we should see many instances where this is not the case.
Higher scores are more favorable for both Udder Suspension and Teat Size EPDs.

This is an example of publish it and they will come; from the Spring 2015 and Fall 2015 evaluations 25,000 records were added to the Hereford udder and teat data set.

Repeated measures on females are included in this analysis. Scoring system is designed for characterizing udder quality - not milk production levels.
[My question, is there an optimal level for udder suspension? If the udder is too tight, will milk production suffer?]
The contemporary group records account for subtle differences between how different farmers and ranchers score the udders and teats.

The purpose of scoring udders is to provide commercial producers with problem-free genetics. Producers are encourages to score udders when taking calf's birth weights.
When scoring, 9 is favorable and 1 is unfavorable. Be consistent in scoring within your cow group and herd. In scoring, suspension is always the first number and teat score is the second number.

Udder scores should be collected within 24 hours of calving. Udders should be scored annually. Contemporary groups account for herd, year, and season difference in scoring.
Keep scoring independent of milk production levels.

See the Udder Scoring Fact Sheet for more information.

Northcutt encouraged Hereford breeders, saying "You have some exciting new traits."

Tuesday, November 10, 2015

Angus Genetics Inc. Updates to EPD/Pedigree Lookup

Based on input and requests from breeders, we’ve been working on some updates to the information displayed on the Animal Search feature on Angus.org. These new features went live this morning [10 November 2015], and I want to take a minute to highlight and explain these enhancements.
  • Genomic Progeny 
  • EPD percentile ranks
  • Progeny 
For complete post, please visit Angus Genetics Inc blog, and read the post by Dr. Tonya Amen.

Decker's Take Home: I always love to see breed associations changing and innovating. I think these changes will allow producers to more quickly evaluate an animal's genetic merit. Plus, I'm sure breeders appreciate AGI responding to requests.


Thursday, November 5, 2015

The Power of the Genome: Weighing Opportunities, Dangers and Responsibility

Angus Convention 2015


Richard Resnick
CEO of GenomeQuest

One can not impede scientific progress.
- Mahmoud Ahmadinejad 
Resnick gave a series of examples of how genomics is changing society.

Resnick put a nice spin on the typical sequencing cost figure. He overlays Illumina's ($ILMN) stock price on top of the figure.

He went on to explain that the only real differences between humans, cattle, corn, and other species is the proteins they make. The amino acids, the building block of proteins, are actually the same between species.

Resnick used cystic fibrosis as an example of a disease in which genetics has been very important. One DNA variant that causes the disease is called ΔF508. When a person has this variant, the gene produces the protein, but a check and balance in the cell recognizes the protein as not correct and destroys it. A different variant, G551D, is not so severe that the protein is destroyed, but the protein does not function properly. A drug called Kalydeco alters the mis-shaped protein coded by the G551D variant and allows it to function again.

Cancer is a disease of the genome. What we need is molecular names for these cancers. This will allow more individualized treatments of what is biologically wrong.

With these advances in medicine, humans will be living longer and there will be more demand for food. We need to keep in mind, when we digest food, we take the proteins and shred them back up into amino acids.

Genomic prediction allows you to the predict the future with accuracy. This, of course, is not genetic modification in the GMO sense. But, other agricultural species cannot benefit the same from genomic prediction as sexually reproducing organisms.

Bananas don't have sex. The trees are clones of other trees. But, if a disease comes along, you can't breed for the disease resistance in bananas. Oranges face similar disease issues. Most corn has a gene transfected from bacteria that produces a toxin that stops bugs from eating the plant. Most soybeans are now Roundup Ready, meaning we can spray the plant with pesticides, the crop lives and the weeds die. So, we just need to wash the soybeans, and there are no problems with eating these soybeans.

There is actually a gene for apple browning. Scientist took this gene and duplicated it multiple times in the apple genome. When the apple cells see too much of the protein coded by this browning gene, the cells shut down all copies of this gene. Thus, no browning protein, so the apple does not brown!
Aquabounty salmon, is a modified salmon that grows to its mature size in 18 months.

By Kevin586  via Wikimedia Commons
For writers, they moved from pen and paper, to type writers, to word processors, and now to computers with Google and all the other Internet tools. Today in genomics we have the "word processor" figured out. What will happen when we move past the "word processor" of genomics and get to the "Google" stage of genomics?

Many people (20%) find cilantro disgusting, it tastes like soap to them. This disgust is caused by genetics. If you go to a high-end restaurant, wouldn't the chef want to know that you hate cilantro? In fact, a certain food company is doing lots of sequencing in Europe to figure out what foods people like or is more nutritional for them.

The baby's entire genome is circulating in the mother's blood. This means we can test the baby's DNA from the mother's blood. What is the line between aborting a baby for the presence of a horrible disability and aborting a baby for the lack of a preferred trait?

There is a patent for DNA testing to identify sperm donors. "Is this a problem? Certainly not in bovines, but what about humans?" Resnick asked. Previously when we did gene modification, we used a sledge hammer, now with CRISPR technology we can use a precise scalpel. Dehorning is a bad public perception issue, takes time and labor, and is an animal welfare issue. Recombinetics has technology to take an animal with the variant that causes horn growth and to replace it with the gene that causes the animal to be polled.

In the United States, we don't do gene editing in humans due to ethical concerns. But, scientists in China have already worked on altering nonviable human embryos.

"Have I scared you a little bit? Hopefully." Resnick stated. But, he hopes that you now understand the difference between DNA testing (like we do for genomic-enhanced EPDS) and genetic modification, that you understand the impacts genetic modification can have, and that you can intelligently discuss these topics with the rest of society.

For more information on Resnick's talk see Troy Smith's article at AngusConvention.com and Resnick's presentation slides.


Monday, November 2, 2015

Forty-Nine Performance Bulls Average $4581 at the 86th Southwest Missouri Beef Cattle Improvement Association’s Bull Sale

Eldon Cole, Livestock Specialist

The 86th Southwest Missouri Beef Cattle Improvement Association’s bull sale averaged $4581 on 49 bulls.  Leading the average were the 46 Angus bulls that made $4684.  Three Polled Herefords were harder to get bids on and each received a $3000 bid.

The consignment had outstanding performance data behind them and the knowledgeable bidders on the seats found the top prospects throughout the sale.  One thing that stood out again was the reluctance of buyers to go very high on bulls that had calving ease direct expected progeny differences (EPD) that were poorer than breed average.

The sale top of the evening was a May, 2014 Angus consigned by Truman L. Wiles, Willow Springs.  The bulls calving ease, weaning weight and yearling weight ranked him in the first percentile for Angus non-parent bulls.  His $Wean was also in the first percentile.  The 7-framebull brought $7000 from Kevin and Cheryl Dill of Niangua.

Close behind at $6750 was the entry from Blue Mound Angus, Fred Swartzentruber, Eldorado Springs.  Also a 7-frame score bull with EPDs for calving ease, weaning weight, yearling weight, milk $Wean and $Beef in the top 15 percentile or better was claimed by Travis Eck, Pierce City.

Two Angus bulls were sold for $6500 each consigned by Wiles and Norman Garton, Nevada.  The successful buyers were Brackenridge Brothers, Eldorado Springs and Charles Whisman, Shell Knob.  Each of the buyers regularly purchase bulls from this sale.

The three Polled Herefords were consigned by Bonebrake Herefords, Springfield.  The buyers were Two Bar D, Niangua, White’s Bar W Ranch, Ozark and Brian and Tara Wilson, Neosho.

The sale was held on October 26 at the Springfield Livestock Marketing Center.  Auctioneer was Jerry Lehmann, Lake Ozark.  Pam Naylor, Buffalo serves the SW MO BCIA as sale manager.

The next sale will be the last Monday of March.  Consignments for it will begin in late December.  For details on that you may contact Pam at 417-345-8330 or contact your nearest University of Missouri Extension livestock specialist.

More details on the BCIA may be found at www.swmobcia.com 

Sunday, November 1, 2015

Summary of the DNA Technology: Where we've been, where we are, and where we're headed Conference

Meat Animal Research Center, Clay Center, NE

Matt Spangler
University of Nebraska-Lincoln


 Why are we working on these novel traits?
 Because they have great economic importance.
 Further, they have heritable genetic variation.

 We do have EPDs for feed intake and fertility, but they are not as pervasive as other (weight and carcass) traits.

Continued phenotypic data collection and recording is critically needed. But, the breed associations have to do something with the data. Otherwise, progressive seedstock producers will look outside breed associations for genetic evaluations. This will not be a great outcome for commercial cattle producers.

Nine breeds are already incorporating genomic information into EPD, with many other breeds right on the cusp of releasing genomic-enhanced EPDs.

As genotyping becomes more common and more animals are genotyped, many of the current limitations are eliminated. But, there is continued room for statistical approaches to be refined.

 Genotyping entire cohorts (groups) fixes many of the problems.

Many groups are rapidly expanding the amount of cattle genomic sequence data. But, substantial effort will be required to turn this data into deliverables and information for the beef industry.

Please check out beefefficiency.org for more information from the DNA Technology Conference.

Friday, October 30, 2015

Selection for Improved Feed Efficiency

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org

Meat Animal Research Center, Clay Center, NE

Matt Spangler
University of Nebraska-Lincoln


In poultry, we have seen a 250% improvement in feed efficiency since 1957. We have dramatically improved the efficiency of gain in chickens.

We have not made similar progress in beef cattle. How can we move the needle and start to make progress?

First of all, how do we define feed efficiency?

  • Average daily gain (ADG)
  • Average daily feed intake (AFI)
  • Residual feed intake (RFI) is the difference between what we expected an animal to eat and what they actually ate. In residual feed intake, how we define a contemporary group is very important. For example, think of combining Scottish Highland and Chianina cattle in a group. 


EPDs for feed efficiency

  • Residual gain
  • residual feed intake
  • dray matter intake
  • Days to finish


If a breed publishes multiple efficiency EPDs, which one do I choose?
Hint: The answer comes below! Spoiler alert, economic indexes!

Getting feed intake records can be very expensive. It is probably not feasible for a large number of feed intake phenotypes to enter national cattle evaluation. Genomics helps us collect phenotypes on
a manageable number of animals and use that data to predict feed intake in a much larger population.

With genomic testing, we can account for a large portion of the genetic variation in feed intake and about 30 to 40% of the overall variation in feed intake (phenotypic variation).

The largest effect genes in feed intake

We want to select for the most profitable animals. We don't want the most productive cattle or the most efficient cattle, but the cattle that best combine production and efficiency to be profitable.

Depending on how we measure feed efficiency, cattle rank differently.

Do we want to estimate the relationship between two traits? Such as feedlot efficiency and cow efficiency.
Spangler says, "Collect, record, estimate". If producers want to know the answers to these types of questions, they need to turn the data into breed associations.

We need to think about efficiency in terms of economic returns. An economic index approach is the optimal way to make change in many different traits.

"These large USDA grants are a jumping off point for breed associations," Spangler said.
The breed associations and beef industry will then need to create methods to continue to collect the data.

For a video of this talk see the conference website: http://www.beefefficiency.org/annualmtgoct15.html


Thursday, October 29, 2015

Selection for Cattle that are Less Susceptible to BRD

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org

Meat Animal Research Center, Clay Center, NE
Alison Van Eenennaam
University of California-Davis
Twitter: @biobeef


The long-term goal of this project is to reduce the incidence of bovine respiratory disease (BRD) complex through genomic selection. We would not want to challenge our herd to see if they are susceptible or not; too many would end up dead! Genomics helps us select for traits that are difficult to measure or have a low heritability.

But to create genomic predictions we need large populations, e.g. 1000s of animals, with phenotypes (trait measurements) and genotypes. BRD can be difficult to measure and quantify; the data can be noisy. Part of the focus of the project was a very careful definition of a sick animal. Temperature, cough, nasal drainage, eye scores, and ear scores were used to define whether or not an animal was sick. Each morning a researcher would walk down a row of calf hutches to find a sick animal and would take a blood sample. The researcher would then find a calf in an adjacent hutch who was not sick. A similar approach was done in beef cattle feed lots. In California, over 200,000 calves were screened to obtain 1,003 cases (sick) and 1,003 controls (healthy) diary calves. In the dairy cattle, genetics explained 21% of the variation in BDR susceptibility. In the beef cattle, genetics explained 18% of the variation in BRD susceptibility. Curt VanTassel is working on incorporating BRD susceptibility into the dairy economic index ($NetMerit). A SNP chip with 220,000 variants has been developed to test variants that are functional. These variants affect the amount or sequence of a protein. It is hoped that these functional variants within genes will be more predictive of the genetic differences in BRD resistenance. In order to produce genomic-enhanced EPDs, we will need to collect phenotypic data on which animals get sick, and which do not. The logical place to do this is beef feedlots, as they record which animals gets sick. We need to figure out how to make this a win-win situation for feed lots, breed associations, and breeders. Disease predictions are not necessarily low hanging fruit. But, if genetic and genomic predictions are successful, they will have a significant economic impact.

More information about the Bovine Respiratory Disease Coordinated Agriculture Project (BRD CAP) can be found at http://www.brdcomplex.org/.

For a video of this talk see the conference website: http://www.beefefficiency.org/annualmtgoct15.html

Wednesday, October 28, 2015

Selecting for More Fertile Females

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org

Meat Animal Research Center, Clay Center, NE

Jared E. Decker
University of Missouri


Introduction

It has frequently been stated that reproductive traits have low heritabilities, meaning little of the variation in reproductive traits is due to genetic differences. Due to this catchphrase, producers may not emphasize reproductive traits in their breeding decisions. Further, cows and heifers may sometimes receive a “Get Out of Jail, Free” card when their reproductive performance is lacking.
Let us reconsider the amount of variation in reproductive traits due to genetics. First consider the Heifer Pregnancy EPD reported by the American Angus Association. They report a heritability of 14% for Heifer Pregnancy (https://www.angus.org/Nce/Heritabilities.aspx ). At first, this may seem like a very small percentage. But, to put it in further perspective, we can compare it to other traits that receive more attention. Weaning weight, the most consistently selected trait in Angus cattle from 1955 to 2007 (Decker et al., 2012), only has a heritability of 20%. The American Hereford Association reports a heritability of 27% for their Heifer Calving Rate EPD. Thus, there is sufficient genetic variation present to make sustained genetic progress for reproductive traits. Due to the economic importance of reproductive traits, beef farmers and ranchers should consider putting more emphasis on reproduction when making selection decisions. Below, some of the tools available to accomplish this are discussed.

Breed Association EPDs

Expected progeny differences (EPDs) and economic indexes are the preferred method of selection, as they are the most accurate and unbiased tools. Although they are newer than traditional growth EPDs, several breed associations publish fertility EPDs. These can be broadly characterized as heifer success or repeated success EPDs. Selecting for fertility EPDs will increase the reproductive performance of herds, assuming appropriate management practices are used.


Heifer Reproductive Success EPDs


Breed Association
EPD
Units
Description
American Angus Association
Heifer Pregnancy
Percent
Probability of daughters becoming pregnant.
American Hereford Association
Heifer Calving Rate
Percent
Probability of daughters to calve as heifers.
American Gelbvieh Association
Heifer Pregnancy
Percent
Probability of daughters becoming pregnant in a regular breeding season.
Red Angus Association of America
Heifer Pregnancy
Percent
Probability of heifers conceiving to calve at two years of age




Repeated Reproductive Success EPDs

Breed Association
EPD
Units
Description
American Hereford Association
Sustained Cow Fertility
Risk Ratio, lower number favorable
*Now defined as percentage, higher number favorable
Risk of daughter not achieving a calving interval of 425 days or less.
American Gelbvieh Association
30-month pregnancy (Pg30)
Percentage, higher number favorable
Given that a daughter calved as a first-calf heifer, probability that daughter will calve at three years of age.
American Gelbvieh Association
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.
American Simmental Association
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.
North American Limousin Federation
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.
Red Angus Association of America
Stayability
Percentage,
higher number favorable
Percent of daughters staying in the cowherd at 6 years of age.


Phenotypic Selection

In some situations, such as selecting commercial replacement females, EPDs are not available. And, of course, all EPD predictions are based on sound phenotype records. Below, we discuss some of the traits that have been beneficial to measure in the Missouri Show-Me-Select Heifer Replacement Program. In the program, a prebreeding evaluation is required 4 to 6 weeks prior to breeding for all yearling-age heifers, and includes animal identification, weight, pelvic area measurement and reproductive tract score. We also require a pregnancy examination within 90 days from the start of the breeding season.

Culling Open Females

One of the most common selection practices to improve herd fertility is to simply cull open cows. For herds looking to improve reproductive performance, this will continue to be an effective strategy.

Reproductive Tract Score

Reproductive tract scores are used to access the puberty status of heifers for selection decisions and timing of estrous synchronization. Based on rectally examining the uterus and ovaries, heifers are given a 1 to 5 score corresponding to prepubertal/infantile tract, prebubertal/greater than 30 days to puberty, peripubertal/less than 30 days to puberty, pubertal, pubertal/has already ovulated.


Pelvic Area

Pelvic measurements can be used successfully to identify abnormally small or abnormally shaped pelvises.  These situations, left unidentified, often are associated with extreme calving difficulties. Because pelvic growth is strongly influenced by puberty, pelvic area may also be an indicator of puberty status.


Ultrasound Pregnancy Diagnosis

An initial pregnancy examination should be performed within 90 days from the start of the breeding season.  Individual animal identification, pregnancy status and fetal age (in days) should be recorded.  Herds utilizing artificial insemination should report breeding dates.  Pregnancy determination at this point relative to the start of the breeding period enables the veterinarian to more accurately determine fetal age and success of the heifer’s first breeding period.

Future Research

Opportunities exist to research the genetics and genomics of heifer fertility. Reproductive tract scores may be an important indicator trait to more reliably predict heifer pregnancy or heifer calving rate EPDs. A Beef Improvement Federation committee has also been formed to improve the recording and reporting of female reproductive data.


Selecting for More Fertile Females - Dr. Jared Decker, University of Missouri from Iowa Beef Center on Vimeo.

*Post updated on 10 November 2015 to reflect new definition of Sustained Cow Fertility.

Speaker Sensation at the National Angus Convention

Entertaining and educational, an impressive line-up headlines Angus events Nov. 3-5 in Overland Park, Kan.



The complete program for the 2015 Angus Means Business National Convention & Trade Show, which takes place Nov. 3-5 in Overland Park, Kan., features an incredible slate of speakers.

Highlights of the week’s events include an International Angus Genomics Symposium on Tuesday, Nov. 3, sponsored by Neogen®’s GeneSeek Operations, during which keynote speaker and genetics pioneer Richard Resnick will discuss the evolving progress of genomic technology. The afternoon will provide hands-on Genomics Innovation Workshops sponsored by Zoetis.

On Wednesday, Nov. 4, Angus University, sponsored by Merck Animal Health, returns to follow “A Story of a Steak” and share insights on increasing quality in the nation’s beef production chain. Ken Schmidt, former Harley-Davidson communications director is the morning keynote speaker. The afternoon will feature 21 educational breakouts with emphasis on management, animal health, advertising and marketing, commercial cattle production, ag markets, social media training and low-stress cattle demonstrations.

In response to attendee feedback, there will be a few repeated sessions so there is a better chance of attending all desired sessions.

“We are incredibly proud of the slate of education and entertainment available at the 2015 National Angus Convention,” says Becky Weishaar, Creative Media director and lead contact for the event. “We encourage cattle producers to reserve their place in advance of the early registration deadline of October 2 for only $75 per person. Hotel reservations are also made on the convention website, and the hotel block features a variety of price points and amenities on a first-come, first-serve basis.”

Registration increases to $125 per person from Oct. 3 to Oct. 16. After that date, advance registration will be closed and participants may register onsite for $150 per person. Delegates elected to represent their state during the Association’s Annual Convention may attend the Association business meetings for free; however, participation in convention education, meals, entertainment and trade show requires a full convention registration.

Go online to www.angusconvention.com to access a convention schedule, trade show map and more information on travel arrangements to Overland Park, Kan.

Listed below is a summary of featured education at the 2015 Angus Means Business National Convention & Trade Show.



ANGUS MEANS BUSINESS. The American Angus Association is the nation’s largest beef breed organization, serving nearly 25,000 members across the United States and Canada. It provides programs and services to farmers, ranchers and others who rely on the power of Angus to produce quality genetics for the beef industry and quality beef for consumers.

For more information about Angus cattle and the American Angus Association’s programs and services, visit www.ANGUS.org.

###

National Angus Convention & Trade Show

Schedule at a Glance | Nov. 3-5, Overland Park, Kan.



Tuesday, Nov. 3



7 a.m.-7 p.m. — Registration open



9 a.m.-Noon — International Angus Genomics Symposium sponsored by Neogen’s GeneSeek Operations

Keynote, Richard Resnick

Future of Angus Genomics panel: Brian McCulloh, Bill Rishel, Michael Bishop, Illumina; Dan Moser, moderator Ronnie Green

Featured Speaker, Mitch Abrahamsen, Cobb-Vantress



Noon-1:30 p.m. — Trade Show Grand Opening featuring Certified Angus Beef® (CAB) lunch



1:30-5:30 p.m. — Innovation Workshops: Technology & Scientific Advancements for Cattlemen



1:30-3 p.m. — Purebred Angus Genomics Cattle Demonstrations sponsored by Zoetis Animal Health

HD50K, Kent Andersen, Zoetis, and Mark McCully, Certified Angus Beef LLC



3-4 p.m. — Innovation Workshops sponsored by E.I. Medical Imaging, Merial, Angus Genetics Inc. and AAA Login



4-5:30 p.m. — Commercial Angus Genomics Cattle Demonstrations sponsored by Zoetis Animal Health GeneMax® Advantage™ and GeneMax Focus™

Kent Andersen and Mark McCully



5-7 p.m. — Trade Show Social



6:30 p.m. — Cat® 262D Skid Steer Giveaway



Wednesday, Nov. 4



7 a.m.-7 p.m. Registration open



7:30-8:30 a.m. — Angus Auxiliary Breakfast (optional — additional $25 registration)



8:30-10 a.m. — American Angus Association Board of Directors candidate forum



10 a.m.- 7 p.m. — Trade Show open



10 a.m.-12:30 p.m. — Angus University sponsored by Merck Animal Health

Emcee, John Stika, Certified Angus Beef LLC

Keynote, Ken Schmidt

Individual Branding panel: Bob McClaren, 44 Farms, Cameron, Texas; Jonathan Perry, Deer Valley Farms, Fayetteville, Tenn.; Eric Grant, Angus Media; John Stika, moderator



12:30-2 p.m. — Lunch in trade show featuring CAB



2-5 p.m. — Angus University Workshops sponsored by Merck Animal Health



Management

2-2:50 p.m. Maternal Plus

Richard Tokach, Tokach Angus Ranch; Matt Perrier, Dalebanks Angus; Tonya Amen, Angus Genetics Inc.; moderator Dan Moser

3-3:50 p.m. Maternal Plus (repeat)

Richard Tokach, Tokach Angus Ranch; Matt Perrier, Dalebanks Angus; Tonya Amen, Angus Genetics Inc.; moderator Dan Moser

4-4:50 p.m. Succession and Estate Planning

Bill Sheets, Colorado State University



Animal Health

2-2:50 p.m. Healthy Bulls & Females for Your Customers

Mark Spire, Merck Animal Health; Randall Spare, Ashland Veterinary Center Inc.

3-3:50 p.m. Start them off right. Healthy cows raise healthy calves

Kevin Hill, Merck Animal

4-4:50 p.m. Start them off right. Healthy cows raise healthy calves (repeat)

Kevin Hill, Merck Animal



Marketing

2-2:50 p.m. Data-driven Marketing

Eric Grant, Angus Media

3-3:50 p.m. Data-driven Marketing (repeat)

Eric Grant, Angus Media

4-4:50 p.m. Adding Value to Your Customer’s Commercial Herd

Art Butler, Spring Cove Ranch; Dave Rutan, Morgan Ranches; moderator, Ginnette Gottswiller, American Angus Association



Commercial Cattle Production in 21st Century

2-2:50 p.m. How to Build the Perfect Steer

Paul Dykstra, Certified Angus Beef LLC

3-3:50 p.m. Top 10 Things I Learned from Feeding My Cattle

Justin Sexten, Certified Angus Beef LLC; Jimmy Moore, Moore Cattle Co.; Darrel Busby, Tri-County Steer Carcass Futurity; Shane Tiffany, Tiffany Cattle Co.; and Paul Dykstra, Certified Angus Beef LLC

4-4:50 p.m. Fitting Angus Genetics Into Your Environment

Megan Rolf, Oklahoma State University; Mark Enns, Colorado State University; Jared Decker, University of Missouri; moderator Dan Moser



CattleFax

2-2:50 p.m. Market Outlook

Lance Zimmerman, CattleFax

3-3:50 p.m. Market Outlook (repeat)

Lance Zimmerman, CattleFax

4-4:50 p.m. Risk Management

Lance Zimmerman, CattleFax





Responsible Beef

2-2:50 p.m. Farming Your Social Community?

Michelle Payn-Knoper, Cause Matters

3-3:50 p.m. Championing Agriculture

Michelle Payn-Knoper, Cause Matters

4-4:50 p.m. Championing Agriculture (repeat)

Michelle Payn-Knoper, Cause Matters



Creating Connections: Working together for cattle well-being cattle demonstrations

2-2:50 p.m. Stockmanship at Work

Tom Noffsinger

3-3:50 p.m. Low-stress Cattle Acclimation

Tom Noffsinger

4-4:50 p.m. Low-stress Cattle Acclimation (repeat)

Tom Noffsinger



5-7 p.m. — KC Blues & BBQ Social Hour & Dinner featuring Jack Stacks BBQ



7 p.m. — Entertainment: Sammy Kershaw



Thursday, Nov. 5



7 a.m.-Noon — Registration open



7:30-9 a.m. — Awards Breakfast (optional – additional $25 registration)



10 a.m.-2 p.m. — 132nd Annual Meeting of Delegates





For a complete schedule of events at the National Angus Convention, please visit www.angusconvention.com and click on “Schedule.”

Wednesday, October 14, 2015

What have we learned from sequencing efforts to date?

And where are we going next?

Data via http://www.genome.gov/sequencingcosts/.
Code for generating the plot at https://missouri.box.com/SequencingCost.

This graph never ceases to amaze me. On the horizontal axis we have dates from September 2001 to July 2015. On the vertical axis we have the cost to sequence a million base pairs of DNA, with the axis having a logarithmic scale (each tick mark is multiplied by 10, e.g. change from 10 to 100 to 1000). The blue line describes what is called Moore's Law which describes the increase in purchasing power as computer costs come down. The rate of improvement in DNA sequencing easily outpaces the improvement in computing. Since September 2001, the price of DNA sequencing has dropped 6 orders of magnitude from $5,292.39 to $0.015. From more than $5,000 to less than 2 cents!!!

Same data as above by with the vertical cost axis
 on a normal scale, not logarithmic.
What caused the drop in sequencing from April 2015 to July 2015? This is due to the release of the Illumina HiSeq X Ten system. Previously this system was only licensed for human sequencing. But on October 6th, this restriction was lifted and this system is now available for livestock genomics (and other applications). This means we can now sequence cattle genomes for a little more than a $1,000.


What do we plan to do with this decreased sequencing cost? Sequence a lot of bulls and cows of course! As we started to look at this sequence data, what have we found? First of all, we find a lot of DNA variants. In fact, we find similar numbers of variants to when we sequence human genomes. But in cattle we find many common variants (at a moderate frequency in the population) whereas in humans we find many rare variants (very low frequency in the population). This is because humans had a very small number of parents in the past (small effective population size) and a growing number of parents since that time (increasing effective population size). 
Cartoon of changes in population structure of humans
and cattle.
Cattle have the opposite pattern. The wild ancestors of cattle (aurochs) had a very large population in the past with a large number of parents (large effective population size), and through the processes of domestication, selection, and breed formation the effective population size has decreased. Think about how many times you find the same popular bulls in your cattle's pedigrees; this makes the effective population size smaller. This small effective population size with a large number of common variants is what makes downstream uses, like genomic-enhanced EPDs, of genomic data so effective in cattle.

So what are the downstream analyses of genomic data? Well there are lots, too many to mention in this post. But one of the first techniques we use in livestock genomics is a process called imputation. I know imputation is another one of those fancy jargon words, but it simply means that we can infer the genotypes at untested DNA variants based on the patterns of tested DNA variants. Now, instead of running our analyses with tens of thousands of DNA variants spread across the DNA like "mile markers", we can analyze millions of variants and get closer to our "points of interest". Using millions of variants we find important regions that we missed in earlier analyses and more precisely identify the regions of DNA that contain the important genes and causal variants that influence our production traits.

Using genomic sequencing data, scientists have identified causal variants for things like genetic defects, variants responsible for pregnancy losses (embryonic lethals), coat color, and horned vs polled. But finding these causal variants is not easy. Rather than being a simple base pair substitution (SNP), these causal variants are frequently structural variants, meaning large chunks of DNA are inserted, deleted, or rearranged.

As we generate more and more whole genome sequence data, we will have new SNP tests (a.k.a. SNP chips or SNP assays) developed. But instead of these SNPs (DNA variants) being evenly spaced like mile markers, they will be concentrated in genes and other functionally important regions. We will see SNP tests that genotype hundreds of thousands of SNPs, which will be mostly used in research settings. The valuable or interesting variants from these research studies can then be put on low density SNP tests. These low density SNP tests will then be more valuable and predictive as they will be focused on functional content, the points of interest.

Another interesting idea is for breed associations to develop programs to sequence the entire DNA of important or popular sires (idea originated with Jerry Taylor). I call this genomic "surveillance." For example, members would pay an extra $1 every time they registered a calf. When a bull has 1,500 registered progeny, he has now earned $1,500 in fees, and the breed association has enough money to sequence his entire genome. This allows breed associations to discover and keep track of new DNA variants that are rising to high frequency in their population. 

The explosion of genomic data will only continue in beef genetics (watch for more on this soon). What an exciting time to be a beef breeder!

See my extension website to download a copy of my PowerPoint, What have we learned from sequencing efforts to date?

Wednesday, October 7, 2015

2015 NBCEC Brown Bagger Series Kicks Off

by Jeffrey Beall
The 2015 National Beef Cattle Evaluation Consortium Brown Bagger series kicked off today. The Brown Bagger is a webinar discussing beef cattle genetics every Wednesday in October at 12:00 Central time. While we've already missed today's webinar, no fear there are more great presentations coming up. Plus, recordings of today's webinar will be available online in the coming weeks.

The theme for this year's series is "Advancing genetic selection in beef cattle: Improving current tools and developing new ones."

The following presentations are scheduled:

Oct 7 Advancements in National Cattle Evaluation Strategies
Host, Dr. Matt Spangler

  • Latest changes to national cattle evaluation systems—Dr. Bob Weaber, Kansas State University
  • Across Breed EPD and multi-breed genetic evaluation developments—Dr. Larry Kuehn, USDA-ARS-US-Meat Animal Research Center


Oct 14 Beef Cattle Fertility Project and Sequencing Effort Update
Host, Dr. Darrh Bullock

  • Update on USDA Fertility Project—Dr. Megan Rolf, Oklahoma State University
  • What we have learned from sequencing efforts to date—Dr. Jared Decker, University of Missouri


Oct 21 New Beef Improvement Federation Guidelines: Development Update
Host, Dr. Matt Spangler

  • Beef Improvement Federation Feed Intake Guidelines Update—Dr. Mark Enns, Colorado State University
  • Beef Improvement Federation Bovine Respiratory Disease Guidelines Update—Dr. Alison Van Eenennaam, University of California-Davis


Oct 28 Genomically Enhanced EPD Evaluations and New Genetics Educational Resources
Host, Dr. Bob Weaber

  • Status update on genomically enhanced genetic evaluation by breeds—Dr. Matt Spangler, University of Nebraska-Lincoln
  • eBEEF: a beef cattle breeding and genetics resource for producers on eXtension—Dr. Darrh Bullock, University of Kentucky
  • 2016 Beef Improvement Federation Annual Meeting Invite—Dr. Bob Weaber, Kansas State University


If you will be watching the live webinars (not the recordings) please register online via https://kstate.qualtrics.com/SE/?SID=SV_etHw1WTZttuldIx.

Wednesday, September 23, 2015

MU Thompson Research Center event shows new beef genomics, AI breeding

Duane Dailey
Senior Writer, University of Missouri

SPICKARD, Mo. - It has happened before, but always surprises. The biggest, best-looking beef cows had the worst genetic scores.

At the University of Missouri Thompson Farm Field Day, eight cows were sorted out for study by farm visitors. Four cows were top of the herd. Four were on the bottom.

They were sorted on genetic value scores from DNA testing. Cows that looked the best to visitors who didn't know the scores were large frame in good condition, but their calves at side were light-muscled and less fleshy.

Jared Decker, MU Extension geneticist, said the bottom-scoring cows were ready to "go on down the road." They will be replaced by heifers from high-scoring younger cows.

The soon-to-be cull cows had not produced prime-grade calves like the high-scoring cows, Decker said.

Farm manager Jon Schreffler agreed with results from the GeneMax Advantage tests. The high-scoring cows also had high scores in herd records he keeps to track profitable cows on the farm.

Earlier in the field day, Sept. 15 at the farm in northwestern Grundy County, Decker told of genomic testing. All females in the MU Thompson cow herd were genotyped. Commercial testing services determine the DNA profile based on a few drops of blood.

With new technology, top animals can be found early in life before producing their first calf.

David Patterson, MU beef reproduction specialist, told of research at the farm since 1998. His experiments refined use of fixed-time artificial insemination. Now those AI protocols are used on farms nationwide, even worldwide, he said.

Patterson's graduate students told of new research to refine AI breeding.

With fixed-time AI, all cows in a herd can be bred in one morning. That results in less labor and uniform calf crops at weaning and marketing. All MU steers are sent to a feedlot for finishing.

That's when cutout sheets come back from packing plants showing that Thompson calves now rate prime and high choice by USDA graders.

In current quality beef trade, premium prices are paid by packers for high- grade carcasses. More producers across Missouri are following that plan to retain ownership so they can collect high beef prices, plus premiums.

Our goal was to improve AI breeding protocols and produce beef for the "white tablecloth trade," Patterson said.

By knowing genetics of cows and herd sires, matings can be matched to improve the herd as well as improve calving ease and other important traits.

Improved maternal genetics led to adoption of the Show-Me-Select Replacement Heifer Program across the state.

After improving development of replacement heifers, it became clear that steer mates to the heifers also had added value, Patterson said.

With progress in genomics, the mapping of DNA of the beef animal, it is possible to study genetics of all animals in the University of Missouri herd.

Allison Meyer, MU ruminant nutritionist, told the need for quality feed for pregnant cows. The cow's diet provides nutrition for prenatal calves.

"The cow's nutrition has lifelong impact on the calf," she said.

With so much late-cut, low-energy hay this year, Meyer urged farmers to test their hay before winter-feeding season. "There's never been a time when a $20 hay test can add so much value to a herd."

Poor hay can lead to cows not breeding next year, she warned.

Farm superintendent Rod Geisert said the field day gave a wide range of topics from economic outlook to prices for timber sold to loggers.

The event ended, on a windy day, with what Geisert called "an exciting controlled burn" on a grass field.

The research farm is part of the MU College of Agriculture, Food and Natural Resources. Information on AI breeding and replacement heifers is available from regional MU Extension livestock specialists.

Tuesday, September 8, 2015

Missouri Red Angus Association Creates Centralized Bull Test

The Missouri Red Angus Association invites all Red Angus breeders large and small, near and far, to participate in a newly established bull test. Come and join the new era of the Missouri Red Angus Association.

Missouri Red Angus Association’s (MORAA) Board of Directors has been evaluating the past methodology for marketing bulls at the April MORAA sale in Springfield. Based on their evaluation and consistent member feedback that the old program was inadequate, a new program has been launched. The board believes this will be an excellent marketing opportunity for Red Angus genetics.

For cattlemen who have an interest in participating in the project, the test is now accepting entries with receiving dates from Oct. 1–15 for bulls born January, February and March of 2015.

Entry-Consignment Fee:
  • $200 per bull
  • Paid at entry to the selected developer
  • Consignor must be a current Missouri Red Angus member


Approved Test Facilities & Developers:

The Missouri Red Angus Association asks breeders to please consider including bulls in this testing opportunity. Additional information is also available on the Missouri Red Angus website.

For additional information contact:
Kelly Massey, Secretary
(417) 962-0181
Adapted from Red Angus Association of America press release.

Tuesday, September 1, 2015

The Random Shuffle of Genes: Putting the E in EPD



Please see the fact sheet for more information about the random shuffle of chromosomes and genes that happens between generations. This random shuffle explains the differences between full siblings, e.g. flush mates, and the low reliability of traditional EPDs for young animals.